/*=========================================================================
 *
 *  Copyright UMC Utrecht and contributors
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *        http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef __elxPCAMetric2_H__
#define __elxPCAMetric2_H__

#include "elxIncludes.h" // include first to avoid MSVS warning
#include "itkPCAMetric2.h"

#include "itkAdvancedBSplineDeformableTransform.h"
#include "itkStackTransform.h"

namespace elastix
{
/** \class PCAMetric2
 * \brief
 *
 * This metric is based on the AdvancedImageToImageMetric.
 * It is templated over the type of the fixed and moving images to be compared.
 *
 * This metric computes the sum of variances over the slowest varying dimension in
 * the moving image. The spatial positions of the moving image are established
 * through a Transform. Pixel values are taken from the Moving image.
 *
 * This implementation is based on the AdvancedImageToImageMetric, which means that:
 * \li It uses the ImageSampler-framework
 * \li It makes use of the compact support of B-splines, in case of B-spline transforms.
 * \li Image derivatives are computed using either the B-spline interpolator's implementation
 * or by nearest neighbor interpolation of a precomputed central difference image.
 * \li A minimum number of samples that should map within the moving image (mask) can be specified.
 *
 * \parameter SampleLastDimensionRandomly: randomly sample a number of time points to
 *    to compute the variance from. When set to "false", all time points are taken into
 *    account. When set to "true", a random number of time points is selected, which can
 *    be set with parameter NumSamplesLastDimension. \n
 * \parameter NumSamplesLastDimension: the number of random samples to take in the time
 *    time direction of the data when SampleLastDimensionRandomly is set to true.
 * \parameter SubtractMean: subtract the over time computed mean parameter value from
 *    each parameter. This should be used when registration is performed directly on the moving
 *    image, without using a fixed image. Possible values are "true" or "false".
 * \parameter NumEigenValues: number of eigenvalues used in the metric: sum(e) - e, where sum(e)
 *  is the sum of all eigenvalues and e is the sum of the first highest NumEigenValues eigenvalues.
 *
 * \ingroup RegistrationMetrics
 * \ingroup Metrics
 */

template< class TElastix >
class PCAMetric2 :
  public itk::PCAMetric2<
  typename MetricBase< TElastix >::FixedImageType,
  typename MetricBase< TElastix >::MovingImageType >,
  public MetricBase< TElastix >
{
public:

  /** Standard ITK-stuff. */
  typedef PCAMetric2 Self;
  typedef itk::PCAMetric2<
    typename MetricBase< TElastix >::FixedImageType,
    typename MetricBase< TElastix >::MovingImageType > Superclass1;
  typedef MetricBase< TElastix >                       Superclass2;
  typedef itk::SmartPointer< Self >                    Pointer;
  typedef itk::SmartPointer< const Self >              ConstPointer;

  /** Method for creation through the object factory. */
  itkNewMacro( Self );

  /** Run-time type information (and related methods). */
  itkTypeMacro( PCAMetric2, itk::PCAMetric2 );

  /** Name of this class.
   * Use this name in the parameter file to select this specific metric. \n
   * example: <tt>(Metric "PCAMetric2")</tt>\n
   */
  elxClassNameMacro( "PCAMetric2" );

  /** Typedefs from the superclass. */
  typedef typename
    Superclass1::CoordinateRepresentationType              CoordinateRepresentationType;
  typedef typename Superclass1::ScalarType                 ScalarType;
  typedef typename Superclass1::MovingImageType            MovingImageType;
  typedef typename Superclass1::MovingImagePixelType       MovingImagePixelType;
  typedef typename Superclass1::MovingImageConstPointer    MovingImageConstPointer;
  typedef typename Superclass1::FixedImageType             FixedImageType;
  typedef typename Superclass1::FixedImageConstPointer     FixedImageConstPointer;
  typedef typename Superclass1::FixedImageRegionType       FixedImageRegionType;
  typedef typename Superclass1::FixedImageSizeType         FixedImageSizeType;
  typedef typename Superclass1::TransformType              TransformType;
  typedef typename Superclass1::TransformPointer           TransformPointer;
  typedef typename Superclass1::InputPointType             InputPointType;
  typedef typename Superclass1::OutputPointType            OutputPointType;
  typedef typename Superclass1::TransformParametersType    TransformParametersType;
  typedef typename Superclass1::TransformJacobianType      TransformJacobianType;
  typedef typename Superclass1::InterpolatorType           InterpolatorType;
  typedef typename Superclass1::InterpolatorPointer        InterpolatorPointer;
  typedef typename Superclass1::RealType                   RealType;
  typedef typename Superclass1::GradientPixelType          GradientPixelType;
  typedef typename Superclass1::GradientImageType          GradientImageType;
  typedef typename Superclass1::GradientImagePointer       GradientImagePointer;
  typedef typename Superclass1::GradientImageFilterType    GradientImageFilterType;
  typedef typename Superclass1::GradientImageFilterPointer GradientImageFilterPointer;
  typedef typename Superclass1::FixedImageMaskType         FixedImageMaskType;
  typedef typename Superclass1::FixedImageMaskPointer      FixedImageMaskPointer;
  typedef typename Superclass1::MovingImageMaskType        MovingImageMaskType;
  typedef typename Superclass1::MovingImageMaskPointer     MovingImageMaskPointer;
  typedef typename Superclass1::MeasureType                MeasureType;
  typedef typename Superclass1::DerivativeType             DerivativeType;
  typedef typename Superclass1::ParametersType             ParametersType;
  typedef typename Superclass1::FixedImagePixelType        FixedImagePixelType;
  typedef typename Superclass1::MovingImageRegionType      MovingImageRegionType;
  typedef typename Superclass1::ImageSamplerType           ImageSamplerType;
  typedef typename Superclass1::ImageSamplerPointer        ImageSamplerPointer;
  typedef typename Superclass1::ImageSampleContainerType   ImageSampleContainerType;
  typedef typename
    Superclass1::ImageSampleContainerPointer               ImageSampleContainerPointer;
  typedef typename Superclass1::FixedImageLimiterType      FixedImageLimiterType;
  typedef typename Superclass1::MovingImageLimiterType     MovingImageLimiterType;
  typedef typename
    Superclass1::FixedImageLimiterOutputType               FixedImageLimiterOutputType;
  typedef typename
    Superclass1::MovingImageLimiterOutputType              MovingImageLimiterOutputType;
  typedef typename
    Superclass1::MovingImageDerivativeScalesType           MovingImageDerivativeScalesType;

  /** The fixed image dimension. */
  itkStaticConstMacro( FixedImageDimension, unsigned int,
    FixedImageType::ImageDimension );

  /** The moving image dimension. */
  itkStaticConstMacro( MovingImageDimension, unsigned int,
    MovingImageType::ImageDimension );

  /** Typedef's inherited from Elastix. */
  typedef typename Superclass2::ElastixType          ElastixType;
  typedef typename Superclass2::ElastixPointer       ElastixPointer;
  typedef typename Superclass2::ConfigurationType    ConfigurationType;
  typedef typename Superclass2::ConfigurationPointer ConfigurationPointer;
  typedef typename Superclass2::RegistrationType     RegistrationType;
  typedef typename Superclass2::RegistrationPointer  RegistrationPointer;
  typedef typename Superclass2::ITKBaseType          ITKBaseType;

  /** Typedef's for the B-spline transform. */
  typedef itk::AdvancedBSplineDeformableTransformBase<
    ScalarType, FixedImageDimension >                       BSplineTransformBaseType;
  typedef itk::AdvancedCombinationTransform<
    ScalarType, FixedImageDimension >                       CombinationTransformType;
  typedef itk::StackTransform<
    ScalarType, FixedImageDimension, MovingImageDimension > StackTransformType;
  typedef itk::AdvancedBSplineDeformableTransformBase<
    ScalarType, FixedImageDimension - 1 >                   ReducedDimensionBSplineTransformBaseType;

  /** Sets up a timer to measure the initialization time and
   * calls the Superclass' implementation.
   */
  void Initialize( void ) override;

  /**
   * Do some things before each resolution:
   * \li Set CheckNumberOfSamples setting
   * \li Set UseNormalization setting
   */
  void BeforeEachResolution( void ) override;

protected:

  /** The constructor. */
  PCAMetric2(){}
  /** The destructor. */
  ~PCAMetric2() override {}

private:

  /** The private constructor. */
  PCAMetric2( const Self & ); // purposely not implemented
  /** The private copy constructor. */
  void operator=( const Self & );              // purposely not implemented

};

} // end namespace elastix

#ifndef ITK_MANUAL_INSTANTIATION
#include "elxPCAMetric2.hxx"
#endif

#endif // end #ifndef __elxPCAMetric2_H__
